Allow to optionally build stochastic_physics

.github/workflows/build_mpas.yml

@@ -11,7 +11,7 @@ jobs:
       fail-fast: false  # Disable fail-fast
       matrix:
         fortran-compiler: [gfortran-12]
-        build-system: [make]###, cmake]
+        build-system: [make] ###, cmake]
 
     # Environmental variables
     env:
@@ -37,7 +37,7 @@ jobs:
     - name: Install NetCDF library
       run: |
         sudo apt-get update
-        sudo apt-get install libnetcdff-dev liblapack-dev libblas-dev
+        sudo apt-get install libnetcdff-dev
 
     - name: Cache openmpi
       id: cache-openmpi
@@ -138,18 +138,6 @@ jobs:
         echo "LD_LIBRARY_PATH=${PNETCDF}/bin:$LD_LIBRARY_PATH" >> $GITHUB_ENV
         echo "PATH=${PNETCDF}/bin:$PATH" >> $GITHUB_ENV
 
-    - name: Setup NetCDF
-      run: |
-        NETCDF_DIR=/home/runner/NetCDF
-        mkdir -p ${NETCDF_DIR}/lib ${NETCDF_DIR}/include
-        for f in /usr/include/netcdf*.h /usr/include/netcdf*.inc /usr/include/netcdf*.mod; do
-          [ -e "$f" ] && ln -sf "$f" ${NETCDF_DIR}/include/ || true
-        done
-        for f in /usr/lib/x86_64-linux-gnu/libnetcdf*.so; do
-          [ -e "$f" ] && ln -sf "$f" ${NETCDF_DIR}/lib/ || true
-        done
-        echo "NETCDF=${NETCDF_DIR}" >> $GITHUB_ENV
-
 #    - name: Setup environment
 #      run: |
 #        echo "FC=mpif90" >> $GITHUB_ENV

.github/workflows/build_mpas_intel.yml

@@ -41,7 +41,6 @@ jobs:
         install-mpi: true
         install-oneapi: false
         mpi-wrapper-setup: classic
-        install-mkl: true
 
     - name: Cache Intel
       id: cache-INTEL
@@ -50,18 +49,6 @@ jobs:
         path: /opt/intel/oneapi/mpi/2021.10.0
         key: cache-Intel-MPI-${{matrix.fortran-compiler}}-${{matrix.build-system}}-key
 
-    - name: Install NetCDF-C library
-      run: |
-        sudo apt-get update
-        sudo apt-get install libnetcdf-dev
-
-    - name: Cache NetCDF-Fortran
-      id: cache-netcdf-fortran
-      uses: actions/cache@v4
-      with:
-        path: /home/runner/NetCDF
-        key: cache-NetCDF-Fortran-${{matrix.fortran-compiler}}-${{matrix.build-system}}-key
-
     - name: Cache GNU autotools
       id: cache-AUTOTOOLS
       uses: actions/cache@v5
@@ -137,23 +124,6 @@ jobs:
         echo "LD_LIBRARY_PATH=${AUTOTOOLS}/lib:$LD_LIBRARY_PATH" >> $GITHUB_ENV
         echo "PATH=${PNETCDF}/bin:$PATH" >> $GITHUB_ENV
         echo "LD_LIBRARY_PATH=${PNETCDF}/lib:$LD_LIBRARY_PATH" >> $GITHUB_ENV
-        echo "NETCDF=/home/runner/NetCDF" >> $GITHUB_ENV
-
-    - name: Build NetCDF-Fortran
-      if: steps.cache-netcdf-fortran.outputs.cache-hit != 'true'
-      run: |
-        NETCDF_F_VERSION=4.6.1
-        wget -q https://github.com/Unidata/netcdf-fortran/archive/refs/tags/v${NETCDF_F_VERSION}.tar.gz
-        tar -xf v${NETCDF_F_VERSION}.tar.gz
-        cd netcdf-fortran-${NETCDF_F_VERSION}
-        autoreconf -i
-        FC=mpiifort CC=mpiicc \
-          CPPFLAGS="-I$(nc-config --includedir)" \
-          LDFLAGS="-L$(nc-config --libdir)" \
-          ./configure --prefix=/home/runner/NetCDF
-        make -j 8 install
-        NCLIBDIR=$(nc-config --libdir)
-        ln -sf ${NCLIBDIR}/libnetcdf.so /home/runner/NetCDF/lib/libnetcdf.so
 
     - name: Build MPAS Standalone (make)
       if: matrix.build-system == 'make'

.github/workflows/build_mpas_intel_stoch.yml

@@ -0,0 +1,172 @@
+name: Build (Intel) MPAS Stochastic
+
+on: [pull_request,workflow_dispatch]
+
+jobs:
+  build_mpas_intel:
+
+    # The type of runner that the job will run on
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false  # Disable fail-fast
+      matrix:
+        fortran-compiler: [intel]
+        build-system: [make, cmake]
+
+    # Environmental variables
+    env:
+      driver_ROOT: /home/runner/work
+      AUTOCONF_VERSION: 2.71
+      AUTOMAKE_VERSION: 1.17
+      M4_VERSION: 1.4.19
+      LIBTOOL_VERSION: 2.5.4
+      PNETCDF: /home/runner/PnetCDF
+      AUTOTOOLS: /home/runner/AUTOTOOLS
+      OMPI: /opt/intel/oneapi/mpi/2021.10.0
+
+    # Workflow steps
+    steps:
+
+    - name: Checkout code (into ${driver_ROOT})
+      uses: actions/checkout@v6
+
+    - name: Initialize submodules
+      run: |
+        git submodule update --init --recursive
+        echo "ls -l src/core_atmosphere/physics/physics_mmm"
+
+    - name: "Install Intel compilers & MPI"
+      uses: NOAA-EMC/ci-install-intel-toolkit@ufs-community-mpas-ci-v2.0
+      with:
+        install-mpi: true
+        install-oneapi: false
+        mpi-wrapper-setup: classic
+        install-mkl: true
+
+    - name: Cache Intel
+      id: cache-INTEL
+      uses: actions/cache@v5
+      with:
+        path: /opt/intel/oneapi/mpi/2021.10.0
+        key: cache-Intel-MPI-${{matrix.fortran-compiler}}-${{matrix.build-system}}-key
+
+    - name: Install NetCDF-C library
+      run: |
+        sudo apt-get update
+        sudo apt-get install libnetcdf-dev
+
+    - name: Cache NetCDF-Fortran
+      id: cache-netcdf-fortran
+      uses: actions/cache@v4
+      with:
+        path: /home/runner/NetCDF
+        key: cache-NetCDF-Fortran-${{matrix.fortran-compiler}}-${{matrix.build-system}}-key
+
+    - name: Cache GNU autotools
+      id: cache-AUTOTOOLS
+      uses: actions/cache@v5
+      with:
+        path: /home/runner/AUTOTOOLS
+        key: cache-AUTOTOOLS-${{matrix.fortran-compiler}}-${{matrix.build-system}}-key
+
+    - name: Build GNU autotools
+      if: steps.cache-AUTOTOOLS.outputs.cache-hit != 'true'
+      run: |
+        wget -q https://ftp.gnu.org/gnu/m4/m4-${M4_VERSION}.tar.gz
+        gzip -dc m4-${M4_VERSION}.tar.gz | tar -xf -
+        cd m4-${M4_VERSION}
+        ./configure --prefix=${AUTOTOOLS} --silent
+        make -s -j 8 install > qout 2>&1
+        make -s -j 8 distclean >> qout 2>&1
+
+        wget -q https://ftp.gnu.org/gnu/autoconf/autoconf-${AUTOCONF_VERSION}.tar.gz
+        gzip -dc autoconf-${AUTOCONF_VERSION}.tar.gz | tar -xf -
+        cd autoconf-${AUTOCONF_VERSION}
+        ./configure --prefix=${AUTOTOOLS} --silent
+        make -s -j 8 install > qout 2>&1
+        make -s -j 8 distclean >> qout 2>&1
+
+        wget -q https://ftp.gnu.org/gnu/automake/automake-${AUTOMAKE_VERSION}.tar.gz
+        gzip -dc automake-${AUTOMAKE_VERSION}.tar.gz | tar -xf -
+        cd automake-${AUTOMAKE_VERSION}
+        ./configure --prefix=${AUTOTOOLS} --silent
+        make -s -j 8 install > qout 2>&1
+        make -s -j 8 distclean >> qout 2>&1
+
+        wget -q https://ftp.gnu.org/gnu/libtool/libtool-${LIBTOOL_VERSION}.tar.gz
+        gzip -dc libtool-${LIBTOOL_VERSION}.tar.gz | tar -xf -
+        cd libtool-${LIBTOOL_VERSION}
+        ./configure --prefix=${AUTOTOOLS} --silent
+        make -s -j 8 install > qout 2>&1
+        make -s -j 8 distclean >> qout 2>&1
+        echo "LD_LIBRARY_PATH=${AUTOTOOLS}/lib:$LD_LIBRARY_PATH" >> $GITHUB_ENV
+        echo "PATH=${AUTOTOOLS}/bin:$PATH" >> $GITHUB_ENV
+
+    - name: Cache PnetCDF
+      id: cache-pnetcdf
+      uses: actions/cache@v5
+      with:
+        path: /home/runner/PnetCDF
+        key: cache-PnetCDF-${{matrix.fortran-compiler}}-${{matrix.build-system}}-key
+
+    - name: Install PnetCDF
+      if: steps.cache-pnetcdf.outputs.cache-hit != 'true'
+      run: |
+        set -x
+        echo "LD_LIBRARY_PATH=${AUTOTOOLS}/lib:$LD_LIBRARY_PATH" >> $GITHUB_ENV
+        echo "PATH=${AUTOTOOLS}/bin:$PATH" >> $GITHUB_ENV
+        m4 --version
+        autoconf --version
+        automake --version
+        libtool --version
+        echo "Install PnetCDF on ${PNETCDF}"
+        rm -rf PnetCDF ; mkdir PnetCDF ; cd PnetCDF
+        git clone -q https://github.com/Parallel-NetCDF/PnetCDF.git
+        cd PnetCDF
+        autoreconf -i
+        ./configure --prefix=${PNETCDF} --with-mpi=${OMPI}
+        make -j 8 install
+        echo "PATH=${PNETCDF}/bin:$PATH" >> $GITHUB_ENV
+
+    - name: Setup environment
+      run: |
+        echo "FC=mpiifort" >> $GITHUB_ENV
+        echo "CC=mpiicc"   >> $GITHUB_ENV
+        echo "PNETCDF=${PNETCDF}" >> $GITHUB_ENV
+        echo "PATH=${AUTOTOOLS}/bin:$PATH" >> $GITHUB_ENV
+        echo "LD_LIBRARY_PATH=${AUTOTOOLS}/lib:$LD_LIBRARY_PATH" >> $GITHUB_ENV
+        echo "PATH=${PNETCDF}/bin:$PATH" >> $GITHUB_ENV
+        echo "LD_LIBRARY_PATH=${PNETCDF}/lib:$LD_LIBRARY_PATH" >> $GITHUB_ENV
+        echo "NETCDF=/home/runner/NetCDF" >> $GITHUB_ENV
+
+    - name: Build NetCDF-Fortran
+      if: steps.cache-netcdf-fortran.outputs.cache-hit != 'true'
+      run: |
+        NETCDF_F_VERSION=4.6.1
+        wget -q https://github.com/Unidata/netcdf-fortran/archive/refs/tags/v${NETCDF_F_VERSION}.tar.gz
+        tar -xf v${NETCDF_F_VERSION}.tar.gz
+        cd netcdf-fortran-${NETCDF_F_VERSION}
+        autoreconf -i
+        FC=mpiifort CC=mpiicc \
+          CPPFLAGS="-I$(nc-config --includedir)" \
+          LDFLAGS="-L$(nc-config --libdir)" \
+          ./configure --prefix=/home/runner/NetCDF
+        make -j 8 install
+        NCLIBDIR=$(nc-config --libdir)
+        ln -sf ${NCLIBDIR}/libnetcdf.so /home/runner/NetCDF/lib/libnetcdf.so
+
+    - name: Build MPAS Standalone (make)
+      if: matrix.build-system == 'make'
+      run: |
+        cd ${driver_ROOT}/MPAS-Model/MPAS-Model
+        make intel-mpi CORE=init_atmosphere
+        make intel-mpi CORE=atmosphere STOCHASTIC_PHYSICS=true AUTOCLEAN=true
+
+    - name: Build MPAS Standalone (cmake)
+      if: matrix.build-system == 'cmake'
+      run: |
+        cd ${driver_ROOT}/MPAS-Model/MPAS-Model
+        mkdir build
+        cd build
+        cmake -DMPAS_DOUBLE_PRECISION=OFF -DSTOCHASTIC_PHYSICS=ON -DMPAS_CORES="init_atmosphere;atmosphere" ..
+        make -j8